Figure 4.

Evaluation of TChAP-seq binding regions. A, Heat map representation of the MACS scores of ChIP, ChAP, and TChAP-seq-identified binding regions. Per method, the MACS scores were transformed to a range between 0 and 1, making it possible to visually compare the relative scores between the different methods. Regions not called in a data set are depicted white. B, Binding of E2Fa to TChAP-unique identified binding regions, having different confidence scores (Supplemental Table S6), was analyzed by quantitative ChIP/ChAP/TChAP PCR. Besides known E2Fa target genes (#), also new identified E2Fa-bound genes were selected. E2F motif genes are indicated with $. Enrichment of E2Fa binding was normalized using CDKA;1 and UBQ10 control promoter regions. Error bars indicate sd (n = 3).